1. Field of the Invention
The present invention relates generally to the use of large circular (LC)-sense molecule as a probe in an array system. The invention also relates to the use of LC-sense molecule library as probes in an array system. In particular, the present invention relates to DNA chip technology, which utilizes arrays having associated single stranded LC-sense molecules. The present invention also describes methods of producing such arrays, assays for using such arrays, kits containing such arrays, and applications thereof.
2. General Background and State of the Art:
Recent developments in DNA microarray technology permits one to monitor a large number of cellular transcripts in a parallel fashion (Schena et al., Science, 270, 467-470 (1995), DeRisi et al., Science, 278, 680-686 (1997), Iyer et al., Science, 283, 83-87 (1999)). Both physiological and pathological changes in the function of cells are associated with alterations of gene expression patterns. For example, development of a malignancy is typically associated with both overexpression of oncogenes and decreased expression of tumor suppressor genes. Identification of differentially expressed genes has been used as a tool to recognize genes that are involved in disease process.
Various methods are available for detecting differentially expressed genes, including northern blot analysis (Alwine et al., Proc. Natl. Acad. Sci., 74, 5350-5354 (1977)), S1 nuclease protection (Berk et al., Cell, 12, 721-732 (1977)), differential display (Liang et al., Science, 257, 967-971 (1992)), sequencing of cDNA libraries (Adams et al., Science, 252, 1651-1656 (1991), Okubo et al., Nature Genet., 2, 173-179 (1992)), serial analysis of gene expression (SAGE) (Velculescu et al., Science, 270, 484-487 (1995)), subtractive hybridization (Hedrick et al., Nature, 308, 149-153 (1984)) and representational difference analysis (RDA) (Hubank et al., Nucleic Acids Res., 22, 5640-5648 (1994), Lisitsyn et al., Science, 259, 946-951 (1993)). But these techniques are limited by the amount of data obtained from one experiment and are time-consuming to perform. Using cDNA array hybridization, the expression of thousands or tens of thousands of genes can be studied simultaneously. This has previously been done by dotting the DNA onto nylon membranes and hybridizing with radioactively labeled cDNA (Augenlicht et al., Proc. Natl. Acad. Sci., 88, 3286-3289 (1991)). Recently, protocols using cDNA microarrays on glass slides, or oligonucleotides on so-called gene chips, together with fluorescent labeled probes, have been introduced (Schena et al., Science, 270, 467-470 (1995), Lockhart et al., Nature Biotechnol, 14, 1675-1680 (1996)).
Despite the wide variety of array technologies that have been developed, there is a continued need to identify new array devices to meet the needs of specific applications.